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ecopcr: fixed a bug where sequences were considered circular (generating

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false positives)
This commit is contained in:
Celine Mercier
2020-04-27 14:44:35 +02:00
parent 60bfd3ae8d
commit 058f2ad8b3
2 changed files with 4 additions and 4 deletions
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2
python/obitools3/version.py
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@ -1,5 +1,5 @@
major = 3 major = 3
minor = 0 minor = 0
serial= '0-beta1c' serial= '0-beta14d'
version ="%d.%02d.%s" % (major,minor,serial) version ="%d.%02d.%s" % (major,minor,serial)

6
src/obi_ecopcr.c
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@ -1061,7 +1061,7 @@ int obi_ecopcr(const char* i_dms_name,
length = 0; length = 0;
if (posj > posi) if (posj > posi)
length = posj - posi - o1->patlen - o2->patlen; length = posj - posi - o1->patlen - o2->patlen;
if (posj < posi) else if (circular > 0)
length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen; length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
if ((length>0) && // For when primers touch or overlap if ((length>0) && // For when primers touch or overlap
(!min_len || (length >= min_len)) && (!min_len || (length >= min_len)) &&
@ -1151,7 +1151,7 @@ int obi_ecopcr(const char* i_dms_name,
length = 0; length = 0;
if (posj > posi) if (posj > posi)
length = posj - posi + 1 - o2->patlen - o1->patlen; /* - o1->patlen : deleted by <EC> (prior to the OBITools3) */ length = posj - posi + 1 - o2->patlen - o1->patlen; /* - o1->patlen : deleted by <EC> (prior to the OBITools3) */
if (posj < posi) else if (circular > 0)
length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen; length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
if ((length>0) && // For when primers touch or overlap if ((length>0) && // For when primers touch or overlap
(!min_len || (length >= min_len)) && (!min_len || (length >= min_len)) &&
@ -1232,7 +1232,7 @@ int obi_ecopcr(const char* i_dms_name,
return -1; return -1;
} }
fprintf(stderr,"\rDone : 100 %% "); fprintf(stderr,"\rDone : 100 %% \n");
return 0; return 0;
return 0; return 0;